Parallelized computational 3D video microscopy of freely moving organisms at multiple gigapixels per second

计算机科学 计算机视觉 人工智能 卷积神经网络 视野 三维重建 帧速率 软件 程序设计语言
作者
Kevin C. Zhou,Mark Harfouche,Colin Cooke,Jaehee Park,Pavan Chandra Konda,Lucas Kreiß,Kanghyun Kim,Joakim Jönsson,Jed Doman,Paul Reamey,Veton Saliu,Clare B. Cook,Maxwell Zheng,Jack P. Bechtel,Aurélien Bègue,Matthew E. McCarroll,Jennifer Bagwell,Gregor Horstmeyer,Michel Bagnat,Roarke Horstmeyer
出处
期刊:Cornell University - arXiv
标识
DOI:10.48550/arxiv.2301.08351
摘要

To study the behavior of freely moving model organisms such as zebrafish (Danio rerio) and fruit flies (Drosophila) across multiple spatial scales, it would be ideal to use a light microscope that can resolve 3D information over a wide field of view (FOV) at high speed and high spatial resolution. However, it is challenging to design an optical instrument to achieve all of these properties simultaneously. Existing techniques for large-FOV microscopic imaging and for 3D image measurement typically require many sequential image snapshots, thus compromising speed and throughput. Here, we present 3D-RAPID, a computational microscope based on a synchronized array of 54 cameras that can capture high-speed 3D topographic videos over a 135-cm^2 area, achieving up to 230 frames per second at throughputs exceeding 5 gigapixels (GPs) per second. 3D-RAPID features a 3D reconstruction algorithm that, for each synchronized temporal snapshot, simultaneously fuses all 54 images seamlessly into a globally-consistent composite that includes a coregistered 3D height map. The self-supervised 3D reconstruction algorithm itself trains a spatiotemporally-compressed convolutional neural network (CNN) that maps raw photometric images to 3D topography, using stereo overlap redundancy and ray-propagation physics as the only supervision mechanism. As a result, our end-to-end 3D reconstruction algorithm is robust to generalization errors and scales to arbitrarily long videos from arbitrarily sized camera arrays. The scalable hardware and software design of 3D-RAPID addresses a longstanding problem in the field of behavioral imaging, enabling parallelized 3D observation of large collections of freely moving organisms at high spatiotemporal throughputs, which we demonstrate in ants (Pogonomyrmex barbatus), fruit flies, and zebrafish larvae.
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